chore: update crates.io publish plan and fix dependencies

- Update CRATES_PUBLISH_PLAN.md with Level 0-2 completion status
- Fix binary-merkle-tree and related dependencies
- Add runtime_logger_tests.rs
- Update various Cargo.toml files

bizinikiwi/primitives/state-machine/Cargo.toml

@@ -36,7 +36,6 @@ trie-db = { workspace = true }
 arbitrary = { features = ["derive"], workspace = true }
 array-bytes = { workspace = true, default-features = true }
 assert_matches = { workspace = true }
-pezsp-runtime = { workspace = true, default-features = true }
 pretty_assertions = { workspace = true }
 rand = { workspace = true, default-features = true }
 
@@ -51,7 +50,6 @@ std = [
 	"pezsp-core/std",
 	"pezsp-externalities/std",
 	"pezsp-panic-handler",
-	"pezsp-runtime/std",
 	"pezsp-trie/std",
 	"rand",
 	"thiserror",
@@ -59,6 +57,5 @@ std = [
 	"trie-db/std",
 ]
 runtime-benchmarks = [
-	"pezsp-runtime/runtime-benchmarks",
 	"pezsp-trie/runtime-benchmarks",
 ]